Common errors and how to fix them

Day 1 - Introduction to Data Analysis with R

Selina Baldauf

Freie Universität Berlin - Theoretical Ecology

October 2, 2023

When learning a programming language, you have to be prepared to spend a lot of your time with fixing bugs in the code. So don’t worry: It’s not you, it’s just how programming works! .footnote-right[Artwork by Allison Horst]

Debugging

Debugging can be annoying and we can’t avoid it, but …

  • … it’s an effective learning experience (I actually learned the most from debugging my code)

  • … it will get easier over time

  • … there are some debugging techniques to decrease the time in stages 2-7

  • … if nothing helps, there are great people all over the internet willing to help

Artwork by Allison Horst

Most common errors for beginners

and how to deal with them class: inverse, center, middle

Syntax errors

Example

mean(c(1,2,3)na.rm=TRUE)

. . .

How to fix

  • look for missing commas, misspelled arguments, …
  • read the error message
  • the RStudio syntax checker warns you before you run code with syntax errors
    • look for    next to line numbers in your script

Error: could not find function

Examples

mutate(penguins, mean = mean(bill_length_mm, na.rm = TRUE))
Error in mutate(penguins, mean = mean(bill_length_mm, na.rm = TRUE)): could not find function "mutate"
lenght(my_vector)
Error in lenght(1:10): could not find function "lenght"

. . .

How to fix

Could not find function errors have two main reasons:

  1. You forgot to load the package that the function belongs to
  • load the package using library() or call the function with packageName::functionName()
  1. You have a typo in your function call (e.g. lenght() instead of length())

Error: object x not found

Example

Error in eval(expr, envir, enclos): object 'hello' not found
Error in eval(expr, envir, enclos): object 'variable_A' not found

. . .

How to fix

  • you are trying to access an object that does not exist
  • Mostly because:
    • typos in variable name (variable name is variableA but you try to access variable_A)
    • forgot to put quotes around string: print(hello) looks for a variable named hello but instead you wanted to print the string print("hello")

Wrong data format

Example

  • does not necessarily trigger an error message

  • if there is an error message, it can also appear later in your code

. . .

How to fix it

  • Look at str() of your data and check whether all columns are there and in correct format
    • e.g. is a column of type character but should be of type integer?
  • Do that at multiple locations in your script to find the line where the error actually happens
    • everytime you change something in your data, check its structure

R crashes

Sometimes R crashes completely and you see this:

How to fix it

  • There is no fix but to start a new session

  • Make sure to save your scripts regularly!

Console prints +

R is not running code anymore and the console only prints + if you try to execute a command.

How to fix it

  • First, go to the console and hit Escape. Then you should see the > sign instead of + again.
  • Likely you forgot to close a bracket somewhere. Go to your script and check where this happened
    • look for    next to line numers

Warnings

R can give you warnings for many reasons, e.g.

  • you have NA values in your data and try to plot them
  • implicit type conversion returned NA
  • the function you are using is deprecated
  • the package you are using was built for another version of R

Warnings are no errors and can sometimes be ignored but:

  • make sure to read and understand warnings
  • only ignore them if you know that that’s okay, otherwise fix the underlying issue

How to troubleshoot R code

A step by step guide

Troubleshoot R: Step by step

Often, you don’t need to do all the steps but a systemmatic approach to bug fixing is very helpful.

Step 1: Carefully read the error message and try to fix it

Step 2: Is it any of the errors you learned about just now?

Step 3: If the error is about data or other variables: look at the structure using str()

Step 4: If the error is about a function: Read the documentation using ?functionName. - Did you use the function correctly? - Did you forget an argument?

Step 5: Look for answers online - often you can also jump directly to this step

Step 6: Ask others for help

Step 5: Look for answers online

  • Search with keywords R + package name + Error message/Warning If you don’t know how do do something try searching R + package name + What you want to do, e.g.
    • “R ggplot change axis title”
    • “R sort vector”
  • Usually you can pick any of the top search results, but I recommend results from Stack Overflow
  • Always search in English to get more results

Tip

Change language of R messages to English with Sys.setenv(LANGUAGE='en')

Step 6: Ask others for help

There are plenty of places where you can ask for help online. Some common and good options are:

But: You have to make sure that before, you tried all the other 5 steps.

To ask questions online, you have to learn how to ask a good R question. This includes:

  • clear question
  • reproducible example

Look here for more info on how to ask a good question about R

Selina Baldauf // Common errors